Sample summary
Input data: infant stools (BS1, BS2, BS3, and BS5) and maternal stool (MS1)
- n samples = 2086
- n taxa: genera = 502; variants = 6372
- n taxa (rarefied): genera = 472; variants = 6235
Statistical methods for mixed-effects models
- Linear mixed-effects models fit with family ID as a random
effect
- Association with ORV outcome determined by comparing fit of model with country/age vs model with age alone
Alpha diversity
Column
Seroconversion
Longitudinal plots - Shannon
Longitudinal plots - richness
Longitudinal plots - E/B ratio
Blue = seroconversion+, Orange = seroconversion-.
P values - E/B ratio
IND
Wilcoxon rank sum test with continuity correction
data: log_Entero_Bac_ratio by seroconv
W = 8673.5, p-value = 0.4668
alternative hypothesis: true location shift is not equal to 0MLW
Wilcoxon rank sum test with continuity correction
data: log_Entero_Bac_ratio by seroconv
W = 230, p-value = 0.1201
alternative hypothesis: true location shift is not equal to 0UK
Wilcoxon rank sum exact test
data: log_Entero_Bac_ratio by seroconv
W = 334, p-value = 0.3457
alternative hypothesis: true location shift is not equal to 0IND neo+
Wilcoxon rank sum test with continuity correction
data: log_Entero_Bac_ratio by seroconv
W = 2956, p-value = 0.0627
alternative hypothesis: true location shift is not equal to 0IND neo-
Wilcoxon rank sum test with continuity correction
data: log_Entero_Bac_ratio by seroconv
W = 1466.5, p-value = 0.3816
alternative hypothesis: true location shift is not equal to 0N by country
, , = IND
BS1 BS2 BS3 BS5
0 208 209 208 202
1 79 76 79 79
, , = MLW
BS1 BS2 BS3 BS5
0 55 56 54 44
1 18 15 12 9
, , = UK
BS1 BS2 BS3 BS5
0 23 24 23 24
1 27 26 25 25
, , = IND (neo+)
BS1 BS2 BS3 BS5
0 108 110 108 111
1 47 46 46 49
, , = IND (neo-)
BS1 BS2 BS3 BS5
0 99 98 99 90
1 32 30 33 30P values, cross-sectional analayses
See Module 5 for full univariate and multivariate analyses.
P values, longitudinal mixed-effects models
Shannon log(Observed)
IND 0.0101 0.0018
IND (neo+) 0.3252 0.3407
IND (neo-) 0.0035 0.0002
MLW 0.5332 0.3367
UK 0.8128 0.5136Sensitivity - exclusively breastfed
Blue = seroconversion+, Orange = seroconversion-.
N by country
, , = IND (neo-), exclusively breastfed
BS1 BS2 BS3 BS5
0 82 82 83 76
1 30 28 30 27P values, longitudinal mixed-effects models
[1] 0.008352455P values, cross-sectional models
week p
1 1 0.0176
2 4 0.0133
3 6 0.0768
4 10 0.9653Sensitivity - vaginal delivery
Blue = seroconversion+, Orange = seroconversion-.
N by country
, , = IND (neo-), vaginal delivery
BS1 BS2 BS3 BS5
0 87 85 86 78
1 22 21 24 23P values, longitudinal mixed-effects models
[1] 0.004111159P values, cross-sectional models
week p
1 1 0.0252
2 4 0.0087
3 6 0.0295
4 10 0.6119Combined plot
Post-ORV RV-IgA
Week of life 1
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0449 -0.0280 -0.1935 0.0002 0.0686
log(richness) -0.0991 -0.1125 -0.2388 -0.1469 0.0488P values
India India_exposed India_unexposed Malawi UK
Shannon 0.4484 0.7290 0.0268 0.9986 0.6361
log(richness) 0.0939 0.1633 0.0060 0.2149 0.7365N
India India_neo_pos India_neo_neg Malawi UK
1 287 155 131 73 50
2 287 155 131 73 50Week of life 4
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0464 -0.0616 -0.1852 0.0726 -0.0592
log(richness) -0.0421 -0.0218 -0.2700 0.1333 -0.0666P values
India India_exposed India_unexposed Malawi UK
Shannon 0.4351 0.4451 0.0363 0.5475 0.6832
log(richness) 0.4785 0.7874 0.0021 0.2678 0.6460N
India India_neo_pos India_neo_neg Malawi UK
1 285 156 128 71 50
2 285 156 128 71 50Week of life 6
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0210 0.0787 -0.1729 -0.3348 -0.0384
log(richness) -0.0609 0.0529 -0.2138 -0.2894 -0.0911P values
India India_exposed India_unexposed Malawi UK
Shannon 0.7228 0.3321 0.0474 0.0060 0.7958
log(richness) 0.3037 0.5147 0.0138 0.0184 0.5382N
India India_neo_pos India_neo_neg Malawi UK
1 287 154 132 66 48
2 287 154 132 66 48Week of life 10
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0469 -0.0433 -0.0427 0.0791 -0.0627
log(richness) -0.0409 0.0501 -0.0752 -0.0329 -0.0044P values
India India_exposed India_unexposed Malawi UK
Shannon 0.4338 0.5870 0.6435 0.5736 0.6687
log(richness) 0.4942 0.5296 0.4144 0.8149 0.9761N
India India_neo_pos India_neo_neg Malawi UK
1 281 160 120 53 49
2 281 160 120 53 49Dose 1 shedding
Longitudinal plots - Shannon
Longitudinal plots - richness
N by country
, , = IND
BS1 BS2 BS3
0 214 208 211
1 73 77 76
, , = MLW
BS1 BS2 BS3
0 29 32 32
1 39 32 25
, , = UK
BS1 BS2 BS3
0 0 0 0
1 0 0 0
, , = IND (neo+)
BS1 BS2 BS3
0 127 126 126
1 26 28 26
, , = IND (neo-)
BS1 BS2 BS3
0 85 80 83
1 46 48 49P values, cross-sectional analayses
See Module 5 for full univariate and multivariate analyses.
P values, longitudinal mixed-effects models
Shannon log(Observed)
IND 0.1729 0.0868
IND (neo+) 0.8628 0.8004
IND (neo-) 0.2459 0.0458
MLW 0.2611 0.1195Beta diversity
Column
Unweighted
Seroconversion
R2 p n country week full outcome
IND_BS1 0.5500733 0.150 287 IND 1 1 seroconversion
IND_BS2 0.5250622 0.164 285 IND 4 1 seroconversion
IND_BS3 0.5030413 0.188 287 IND 6 1 seroconversion
IND_BS5 0.2309698 0.759 281 IND 10 1 seroconversion
MLW_BS1 2.9310572 0.022 73 MLW 1 1 seroconversion
MLW_BS2 1.4137453 0.441 71 MLW 4 1 seroconversion
MLW_BS3 3.5453057 0.025 66 MLW 6 1 seroconversion
MLW_BS5 3.4062591 0.053 53 MLW 10 1 seroconversion
UK_BS1 0.7134424 0.921 50 UK 1 1 seroconversion
UK_BS2 1.5371026 0.634 50 UK 4 1 seroconversion
UK_BS3 2.2358672 0.392 48 UK 6 1 seroconversion
UK_BS5 1.9618925 0.480 49 UK 10 1 seroconversion
INDexp_BS1 0.5738562 0.551 155 IND (neo+) 1 0 seroconversion
INDexp_BS2 0.2444851 0.919 156 IND (neo+) 4 0 seroconversion
INDexp_BS3 0.4977629 0.661 154 IND (neo+) 6 0 seroconversion
INDexp_BS5 0.3269280 0.846 160 IND (neo+) 10 0 seroconversion
INDunexp_BS1 1.7366233 0.042 131 IND (neo-) 1 0 seroconversion
INDunexp_BS2 1.7686967 0.029 128 IND (neo-) 4 0 seroconversion
INDunexp_BS3 1.2315230 0.118 132 IND (neo-) 6 0 seroconversion
INDunexp_BS5 1.6744514 0.035 120 IND (neo-) 10 0 seroconversion
RV-IgA
R2 p n country week full outcome
IND_BS1 0.6292447 0.070 287 IND 1 1 RV-IgA (post-ORV)
IND_BS2 0.1980068 0.804 285 IND 4 1 RV-IgA (post-ORV)
IND_BS3 0.3024169 0.538 287 IND 6 1 RV-IgA (post-ORV)
IND_BS5 0.6028893 0.087 281 IND 10 1 RV-IgA (post-ORV)
MLW_BS1 2.2095504 0.107 73 MLW 1 1 RV-IgA (post-ORV)
MLW_BS2 1.6427758 0.318 71 MLW 4 1 RV-IgA (post-ORV)
MLW_BS3 3.3895945 0.028 66 MLW 6 1 RV-IgA (post-ORV)
MLW_BS5 2.1835129 0.326 53 MLW 10 1 RV-IgA (post-ORV)
UK_BS1 0.3264735 0.979 53 UK 1 1 RV-IgA (post-ORV)
UK_BS2 1.7483228 0.480 53 UK 4 1 RV-IgA (post-ORV)
UK_BS3 2.0692047 0.475 48 UK 6 1 RV-IgA (post-ORV)
UK_BS5 1.4369206 0.701 51 UK 10 1 RV-IgA (post-ORV)
INDexp_BS1 0.9153157 0.193 155 IND (neo+) 1 0 RV-IgA (post-ORV)
INDexp_BS2 0.2280854 0.916 156 IND (neo+) 4 0 RV-IgA (post-ORV)
INDexp_BS3 0.7483168 0.329 154 IND (neo+) 6 0 RV-IgA (post-ORV)
INDexp_BS5 0.8562789 0.214 160 IND (neo+) 10 0 RV-IgA (post-ORV)
INDunexp_BS1 2.0064704 0.011 131 IND (neo-) 1 0 RV-IgA (post-ORV)
INDunexp_BS2 1.1238038 0.190 128 IND (neo-) 4 0 RV-IgA (post-ORV)
INDunexp_BS3 1.2214353 0.114 132 IND (neo-) 6 0 RV-IgA (post-ORV)
INDunexp_BS5 1.5510248 0.056 120 IND (neo-) 10 0 RV-IgA (post-ORV)
Dose 1 shedding
R2 p n country week full outcome
IND_BS1 0.3476460 0.462 287 IND 1 1 dose 1 shedding
IND_BS2 0.2577430 0.648 285 IND 4 1 dose 1 shedding
IND_BS3 0.3835346 0.359 287 IND 6 1 dose 1 shedding
MLW_BS1 1.3418396 0.500 68 MLW 1 1 dose 1 shedding
MLW_BS2 1.9160091 0.277 64 MLW 4 1 dose 1 shedding
MLW_BS3 1.5974604 0.522 57 MLW 6 1 dose 1 shedding
INDexp_BS1 0.1307968 0.980 153 IND (neo+) 1 0 dose 1 shedding
INDexp_BS2 0.8715548 0.234 154 IND (neo+) 4 0 dose 1 shedding
INDexp_BS3 0.7444585 0.363 152 IND (neo+) 6 0 dose 1 shedding
INDunexp_BS1 0.8410342 0.375 131 IND (neo-) 1 0 dose 1 shedding
INDunexp_BS2 0.7048742 0.540 128 IND (neo-) 4 0 dose 1 shedding
INDunexp_BS3 0.9000949 0.292 132 IND (neo-) 6 0 dose 1 shedding
Weighted
Seroconversion
R2 p n country week full outcome
IND_BS1 0.1574865 0.844 287 IND 1 1 seroconversion
IND_BS2 0.9963383 0.017 285 IND 4 1 seroconversion
IND_BS3 0.2530616 0.600 287 IND 6 1 seroconversion
IND_BS5 0.2163289 0.746 281 IND 10 1 seroconversion
MLW_BS1 0.4422911 0.959 73 MLW 1 1 seroconversion
MLW_BS2 1.0286009 0.715 71 MLW 4 1 seroconversion
MLW_BS3 1.6270093 0.358 66 MLW 6 1 seroconversion
MLW_BS5 1.6183212 0.541 53 MLW 10 1 seroconversion
UK_BS1 0.5658089 0.973 50 UK 1 1 seroconversion
UK_BS2 1.0992741 0.813 50 UK 4 1 seroconversion
UK_BS3 2.7201641 0.251 48 UK 6 1 seroconversion
UK_BS5 1.1338328 0.816 49 UK 10 1 seroconversion
INDexp_BS1 0.4404823 0.704 155 IND (neo+) 1 0 seroconversion
INDexp_BS2 1.0807725 0.133 156 IND (neo+) 4 0 seroconversion
INDexp_BS3 0.7024854 0.334 154 IND (neo+) 6 0 seroconversion
INDexp_BS5 0.3730366 0.740 160 IND (neo+) 10 0 seroconversion
INDunexp_BS1 1.0616777 0.230 131 IND (neo-) 1 0 seroconversion
INDunexp_BS2 1.3730370 0.097 128 IND (neo-) 4 0 seroconversion
INDunexp_BS3 0.3989700 0.808 132 IND (neo-) 6 0 seroconversion
INDunexp_BS5 0.5170344 0.773 120 IND (neo-) 10 0 seroconversionRV-IgA
R2 p n country week full outcome
IND_BS1 0.259747270 0.591 287 IND 1 1 RV-IgA (post-ORV)
IND_BS2 0.235555444 0.624 285 IND 4 1 RV-IgA (post-ORV)
IND_BS3 0.187059649 0.789 287 IND 6 1 RV-IgA (post-ORV)
IND_BS5 0.250209280 0.689 281 IND 10 1 RV-IgA (post-ORV)
MLW_BS1 0.041350635 1.000 73 MLW 1 1 RV-IgA (post-ORV)
MLW_BS2 1.191293224 0.581 71 MLW 4 1 RV-IgA (post-ORV)
MLW_BS3 1.124968193 0.630 66 MLW 6 1 RV-IgA (post-ORV)
MLW_BS5 0.973253602 0.828 53 MLW 10 1 RV-IgA (post-ORV)
UK_BS1 0.563487140 0.961 53 UK 1 1 RV-IgA (post-ORV)
UK_BS2 1.613267269 0.562 53 UK 4 1 RV-IgA (post-ORV)
UK_BS3 1.847136338 0.535 48 UK 6 1 RV-IgA (post-ORV)
UK_BS5 0.270076162 0.995 51 UK 10 1 RV-IgA (post-ORV)
INDexp_BS1 0.003460839 0.997 155 IND (neo+) 1 0 RV-IgA (post-ORV)
INDexp_BS2 0.288201200 0.867 156 IND (neo+) 4 0 RV-IgA (post-ORV)
INDexp_BS3 0.927379883 0.204 154 IND (neo+) 6 0 RV-IgA (post-ORV)
INDexp_BS5 0.676041641 0.359 160 IND (neo+) 10 0 RV-IgA (post-ORV)
INDunexp_BS1 1.426836052 0.079 131 IND (neo-) 1 0 RV-IgA (post-ORV)
INDunexp_BS2 0.554642999 0.605 128 IND (neo-) 4 0 RV-IgA (post-ORV)
INDunexp_BS3 0.484489119 0.720 132 IND (neo-) 6 0 RV-IgA (post-ORV)
INDunexp_BS5 0.599110894 0.665 120 IND (neo-) 10 0 RV-IgA (post-ORV)Dose 1 shedding
R2 p n country week full outcome
IND_BS1 0.1417872 0.868 287 IND 1 1 dose 1 shedding
IND_BS2 0.2691645 0.596 285 IND 4 1 dose 1 shedding
IND_BS3 0.1646292 0.832 287 IND 6 1 dose 1 shedding
MLW_BS1 0.8147157 0.846 68 MLW 1 1 dose 1 shedding
MLW_BS2 3.0127436 0.062 64 MLW 4 1 dose 1 shedding
MLW_BS3 1.9326806 0.346 57 MLW 6 1 dose 1 shedding
INDexp_BS1 0.6874234 0.380 153 IND (neo+) 1 0 dose 1 shedding
INDexp_BS2 0.9430243 0.162 154 IND (neo+) 4 0 dose 1 shedding
INDexp_BS3 0.3845373 0.748 152 IND (neo+) 6 0 dose 1 shedding
INDunexp_BS1 1.0834230 0.203 131 IND (neo-) 1 0 dose 1 shedding
INDunexp_BS2 0.3971430 0.821 128 IND (neo-) 4 0 dose 1 shedding
INDunexp_BS3 0.7381359 0.435 132 IND (neo-) 6 0 dose 1 sheddingDifferential taxa
Column
Seroconversion
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
RV-IgA
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
Dose 1 shedding
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
Summary figures
Seroconversion
RV-IgA
Dose 1 shedding
Longitudinal abundance comparisons
Immunogenicity
Number of infants/taxa included in longitudinal models:
- India (full), n infants: 305; n samples: 1140; n taxa: 25
- India (exposed), n infants: 166; n samples: 625; n taxa: 26
- India (unexposed), n infants: 138; n samples: 511; n taxa: 24
- Malawi, n infants: 96; n samples: 263; n taxa: 42
- UK, n infants: 51; n samples: 197; n taxa: 25
India
negatively correlated ns positively correlated
age 6 12 7
IgA 0 25 0
seroconv 0 25 0 taxon Estimate Std.Error padj comparison
1 Bifidobacterium 0.016 0.005 2.954545e-03 age
4 Staphylococcus -0.495 0.011 1.700000e-218 age
6 Veillonella 0.110 0.011 1.550000e-22 age
7 Lactobacillus 0.054 0.011 4.000000e-06 age
9 Haemophilus -0.186 0.011 2.666667e-55 age
10 Klebsiella -0.116 0.012 1.562500e-20 age
11 Enterococcus 0.029 0.012 2.884615e-02 age
13 unassigned_Lachnospiraceae -0.114 0.012 5.714286e-21 age
14 Gemella -0.059 0.010 9.722222e-09 age
15 Enterobacter 0.034 0.011 3.541667e-03 age
18 Clostridium_sensu_stricto_1 -0.154 0.014 2.125000e-26 age
20 Atopobium 0.250 0.010 7.625000e-108 age
21 Actinomyces 0.080 0.008 6.666667e-22 ageSummary statistics
[1] "No significant differences according to ORV outcome"India (exposed)
negatively correlated ns positively correlated
age 7 11 8
IgA 1 25 0
seroconv 0 26 0 taxon Estimate Std.Error padj comparison
1 Bifidobacterium 0.020 0.007 6.145455e-03 age
4 Staphylococcus -0.465 0.016 9.880000e-108 age
6 Veillonella 0.107 0.015 8.450000e-12 age
7 Lactobacillus 0.057 0.013 2.892500e-05 age
9 Haemophilus -0.076 0.015 9.966667e-07 age
10 Klebsiella -0.080 0.016 3.380000e-06 age
12 Rothia 0.039 0.014 1.040000e-02 age
13 unassigned_Lachnospiraceae -0.050 0.017 7.800000e-03 age
14 Gemella -0.048 0.013 6.355556e-04 age
18 Clostridium_sensu_stricto_1 -0.121 0.018 3.172000e-10 age
19 unassigned_Enterobacteriaceae 0.036 0.014 2.228571e-02 age
20 Clostridioides -0.054 0.015 1.040000e-03 age
21 Atopobium 0.241 0.013 8.710000e-57 age
22 Actinomyces 0.147 0.013 3.380000e-24 age
23 Finegoldia 0.100 0.044 3.813333e-02 age
59 Lactobacillus -0.181 0.055 3.640000e-02 IgASummary statistics
taxon Estimate Std.Error padj comparison mean prev
59 Lactobacillus -0.181 0.055 0.0364 IgA 3.685 62.7India (unexposed)
negatively correlated ns positively correlated
age 6 10 8
IgA 0 24 0
seroconv 0 24 0 taxon Estimate Std.Error padj comparison
4 Staphylococcus -0.531 0.016 1.200000e-112 age
6 Veillonella 0.127 0.016 2.948571e-14 age
7 Lactobacillus 0.049 0.017 6.000000e-03 age
8 Collinsella 0.047 0.015 3.138462e-03 age
9 Haemophilus -0.284 0.016 1.560000e-51 age
10 Klebsiella -0.166 0.018 7.200000e-18 age
11 Enterococcus 0.112 0.018 1.333333e-09 age
13 unassigned_Lachnospiraceae -0.168 0.014 2.480000e-26 age
14 Gemella -0.066 0.015 4.000000e-05 age
15 Enterobacter 0.073 0.015 2.880000e-06 age
16 Acinetobacter 0.089 0.014 6.900000e-10 age
18 Clostridium_sensu_stricto_1 -0.218 0.021 1.632000e-22 age
19 Atopobium 0.203 0.018 1.680000e-25 age
24 Peptoniphilus 0.065 0.014 4.363636e-06 ageSummary statistics
[1] "No significant differences according to ORV outcome"Malawi
negatively correlated ns positively correlated
age 11 16 15
IgA 0 42 0
seroconv 0 42 0 taxon Estimate Std.Error padj comparison
1 Bifidobacterium 0.068 0.019 1.085000e-03 age
4 Staphylococcus -0.435 0.026 1.134000e-36 age
5 Bacteroides 0.068 0.019 1.085000e-03 age
7 Lactobacillus 0.103 0.028 7.400000e-04 age
8 Collinsella -0.213 0.026 1.565455e-13 age
9 Haemophilus -0.148 0.023 2.001176e-09 age
10 Klebsiella -0.245 0.027 1.680000e-15 age
12 Rothia 0.181 0.024 1.995000e-11 age
13 unassigned_Lachnospiraceae -0.088 0.023 4.830000e-04 age
18 Enterobacter -0.390 0.037 2.280000e-19 age
21 Enhydrobacter 0.190 0.022 5.460000e-14 age
23 Clostridium_sensu_stricto_1 -0.160 0.024 1.443750e-09 age
24 Phascolarctobacterium -0.100 0.030 1.848000e-03 age
25 Succinivibrio -0.613 0.019 8.820000e-72 age
26 Sutterella -0.168 0.025 3.920000e-10 age
29 Holdemanella 0.093 0.026 8.209091e-04 age
30 Slackia 0.069 0.022 2.746154e-03 age
31 Senegalimassilia 0.128 0.022 9.947368e-08 age
32 Atopobium 0.347 0.022 3.864000e-33 age
33 Actinomyces 0.131 0.023 7.466667e-08 age
34 Lawsonella 0.387 0.022 1.533000e-38 age
35 Finegoldia 0.179 0.021 2.566667e-14 age
36 Ezakiella 0.128 0.018 1.098462e-10 age
39 unassigned_Saccharimonadales -0.309 0.020 3.780000e-33 age
41 Prevotella 0.169 0.024 1.740000e-10 age
42 Peptoniphilus 0.337 0.022 6.230000e-32 ageSummary statistics
[1] "No significant differences according to ORV outcome"UK
negatively correlated ns positively correlated
age 11 10 4
IgA 0 24 0
seroconv 0 25 0 taxon Estimate Std.Error padj comparison
2 Escherichia/Shigella 0.045 0.013 1.750000e-03 age
3 Streptococcus -0.119 0.024 5.312500e-06 age
4 Staphylococcus -0.435 0.025 1.825000e-35 age
9 Haemophilus -0.247 0.024 2.625000e-18 age
10 Klebsiella -0.156 0.020 3.125000e-12 age
11 Enterococcus -0.115 0.024 1.305556e-05 age
14 Gemella -0.120 0.020 3.214286e-08 age
15 Enterobacter -0.050 0.017 6.964286e-03 age
16 Parabacteroides -0.051 0.016 2.500000e-03 age
17 Corynebacterium_1 -0.164 0.023 1.625000e-10 age
20 Granulicatella -0.063 0.015 1.225000e-04 age
22 Actinomyces -0.234 0.032 5.500000e-11 age
23 Eggerthella 0.146 0.018 1.916667e-12 age
24 Negativicoccus 0.058 0.021 1.016667e-02 age
25 Prevotella 0.256 0.078 2.500000e-03 ageSummary statistics
[1] "No significant differences according to ORV outcome"Dose 1 shedding
Number of infants/taxa included in longitudinal models:
- India (full), n infants: 305; n samples: 859; n taxa: 23
- India (exposed), n infants: 164; n samples: 459; n taxa: 24
- India (unexposed), n infants: 138; n samples: 391; n taxa: 22
- Malawi, n infants: 89; n samples: 189; n taxa: 44
- UK, n infants: 60; n samples: 171; n taxa: 21
India
ns
dose1 23Summary statistics
[1] "No significant differences according to ORV outcome"India (exposed)
ns
dose1 24Summary statistics
[1] "No significant differences according to ORV outcome"India (unexposed)
ns
dose1 22Summary statistics
[1] "No significant differences according to ORV outcome"Malawi
negatively correlated ns
dose1 1 42Summary statistics
taxon Estimate Std.Error padj comparison mean prev
28 Sutterella -1.417 0.369 0.01032 dose1 1.28 43.9.
Session info
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] FSA_0.9.3 ALDEx2_1.26.0
[3] zCompositions_1.4.0-1 truncnorm_1.0-8
[5] NADA_1.6-1.1 survival_3.2-13
[7] MASS_7.3-55 sjstats_0.18.1
[9] ggExtra_0.10.0 formattable_0.2.1
[11] NBZIMM_1.0 inlmisc_0.5.5
[13] decontam_1.14.0 ggtree_3.2.1
[15] wesanderson_0.3.6 phangorn_2.8.1
[17] ape_5.6-1 DECIPHER_2.22.0
[19] RSQLite_2.2.12 Biostrings_2.62.0
[21] XVector_0.34.0 cowplot_1.1.1
[23] scales_1.1.1 RVAideMemoire_0.9-81-2
[25] DescTools_0.99.44 ggsignif_0.6.3
[27] binom_1.1-1 shiny_1.7.1
[29] randomcoloR_1.1.0.1 DESeq2_1.34.0
[31] SummarizedExperiment_1.24.0 Biobase_2.54.0
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